Non-invasive prenatal testing reveals copy number variations related to pregnancy complications

Identify gestational diabetes mellitus by deep learning model from cell-free DNA at the early gestation stage

Gestational diabetes mellitus (GDM) is a common complication of pregnancy, which has significant adverse effects on both the mother and fetus. The incidence of GDM is increasing globally, and early diagnosis is critical for timely treatment and reducing the risk of poor pregnancy outcomes. GDM is usually diagnosed and detected after 24 weeks of gestation, while complications due to GDM can occur much earlier. Copy number variations (CNVs) can be a possible biomarker for GDM diagnosis and screening in the early gestation stage. In this study, we proposed a machine-learning method to screen GDM in the early stage of gestation using cell-free DNA (cfDNA) sequencing data from maternal plasma. Five thousand and eighty-five patients from north regions of Mainland China, including 1942 GDM, were recruited. A non-overlapping sliding window method was applied for CNV coverage screening on low-coverage (~0.2×) sequencing data. The CNV coverage was fed to a convolutional neural network with attention architecture for the binary classification. The model achieved a classification accuracy of 88.14%, precision of 84.07%, recall of 93.04%, F1-score of 88.33% and AUC of 96.49%. The model identified 2190 genes associated with GDM, including DEFA1, DEFA3 and DEFB1. The enriched gene ontology (GO) terms and KEGG pathways showed that many identified genes are associated with diabetes-related pathways. Our study demonstrates the feasibility of using cfDNA sequencing data and machine-learning methods for early diagnosis of GDM, which may aid in early intervention and prevention of adverse pregnancy outcomes.

Translation and cross-cultural validation of the non-invasive prenatal testing questionnaire in Arabic

OBJECTIVES

To translate and cross-culturally adapt a Swedish questionnaire to Arabic to assess the awareness of pregnant women in Saudi Arabia regarding the availability of an accurate and safe prenatal screening procedure.

METHODS

The study was conducted at the Obstetrics and Gynecology Clinic, King Abdulaziz Medical City, Riyadh, Saudi Arabia between December 2018 to April 2019. The non-invasive prenatal testing (NIPT) questionnaire, translated and validated in Arabic. Cronbach's alpha reliability testing was carried out to validate the Arabic version of the questionnaire. The sample size was 100 pregnant women, at any gestational period, from 20 to 44 years old. This is a prospective cross-sectional.

RESULTS

An Arabic translated, and culturally validated questionnaire related to the attitudes, knowledge, and self-perceived probability of delivering a child with chromosomal abnormality.  Conclusion: We translated and validated the NIPT questionnaire to assess the attitude and awareness of pregnant women regarding the availability of the NIPT.

Identification of copy number variants by NGS-based NIPT at low sequencing depth

OBJECTIVE

To explore the clinical utility of detecting chromosome copy number variants (CNVs) in the fetus by noninvasive prenatal testing (NIPT) using the low-pass whole-genome sequencing.

METHODS

Eight hundred and seventy-three singleton pregnancies with chromosomal microarray analysis (CMA) available between January 2017 to December 2019 and stored enough plasma sample for NIPT testing were included in this study. The CMA results show that forty-eight pregnancies with CNVs and eight hundred and twenty-five pregnancies are normal. Each pregnancy's plasma sample was blindly tested with NIPT at a depth of 0.51-1.19x for CNVs detection. The performance of the NIPT method for CNVs detection compared with the CMA method is evaluated.

RESULTS

A total of fifty-two CNVs ranging from 0.1-47.3 Mb identified in forty-eight samples were identified by NIPT, of which thirty-four CNVs were consistent with CMA results. Additionally, eighteen CNVs were missed by NIPT. The overall sensitivity and specificity for the detection of CNVs were 65.38% (95% CI: 51.76%-76.89%) and 97.45% (95% CI: 96.12%-98.35%), respectively. However, for the detection of CNVs larger than 2 Mb and CNVs less than 2Mb, the sensitivities were 81.58% (95% CI: 66.27%-91.09%) and 21.43% (95% CI: 6.84%-48.32%), respectively.

CONCLUSION

Our study demonstrated that the NIPT might be an alternative method for screening CNVs comparable with other studies. However, CNVs less than 2Mb in length shows poor sensitivity by NIPT. Noninvasive CNVs detection based on the NIPT method still needs more clinical validation studies and technical improvement to achieve clinically acceptable accuracy.

Counselling for prenatal anomaly screening-A plea for integration of existential life questions

The availability in many countries of new prenatal anomaly screening methods, such as the non-invasive prenatal test (NIPT), and the potential broadening of testing for genetic conditions, creates an ongoing debate about the accompanying existential dilemmas at both societal level and for individual new parents. In many countries, the main goal of counselling for prenatal anomaly screening is to facilitate the reproductive decision-making process of future parents. Therefore, counsellors share information to enable a woman and her partner to think about the pros and cons of participating in screening, try to clarify possible moral dilemmas, and dwell on existential life questions. In line with the CanMEDS framework, healthcare professionals must combine the role of communicator (providing health education) with that of professional (by recognising and responding to existential life questions while facilitating decision-making). This is not easy but it is essential for providing balanced counselling. At present, counselling tends to be sufficient regarding health education, whereas guidance in decision-making, including attention for existential life questions and philosophy of life, offers room for improvement. In this paper, we suggest slowing down and turning the traditional prenatal counselling encounter upside down by starting as a counselling professional instead of a healthcare information sharing communicator and thus making the story of the woman and her partner, within their societal context, the starting point and the basis of the counselling encounter.